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annotate create_reference_dataset.xml @ 22:68494d6aabeb

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Update datamanager and defuse.xml config file generation
author Jim Johnson <jj@umn.edu>
date Thu, 27 Jun 2013 13:11:50 -0500
parents 1af6f32ff592
children 3099cec648e7
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85693cb5339f Correct tool_id create_reference_dataset.xml
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1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="1.6.1">
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2 <description>create a defuse reference from Ensembl and UCSC sources</description>
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3 <requirements>
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4 <requirement type="package" version="0.6.1">defuse</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 <requirement type="package" version="1.0.0">bowtie</requirement>
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7 <requirement type="package" version="2013-05-09">gmap</requirement>
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8 <requirement type="package" version="latest">kent</requirement>
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9 </requirements>
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10 <command interpreter="command"> /bin/bash $defuse_script </command>
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11 <inputs>
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12 <conditional name="genome">
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13 <param name="choice" type="select" label="Select a Genome Build">
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14 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
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15 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
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16 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
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17 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
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18 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
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19 <option value="user_specified">User specified</option>
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20 </param>
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21 <when value="GRCh37">
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22 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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23 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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24 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
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25 <param name="ensembl_version" type="hidden" value="71"/>
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26 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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27 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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28 <param name="ucsc_genome_version" type="hidden" value="hg19"/>
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29 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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30 <param name="mt_chromosome" type="hidden" value="MT"/>
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31 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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32 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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33 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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34 </when>
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35 <when value="NCBI36">
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36 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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37 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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38 <param name="ensembl_genome_version" type="hidden" value="NCBI36"/>
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39 <param name="ensembl_version" type="hidden" value="54"/>
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40 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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41 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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42 <param name="ucsc_genome_version" type="hidden" value="hg18"/>
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43 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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44 <param name="mt_chromosome" type="hidden" value="MT"/>
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45 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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46 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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47 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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48 </when>
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49 <when value="GRCm38">
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50 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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51 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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52 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
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53 <param name="ensembl_version" type="hidden" value="71"/>
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54 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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55 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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56 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
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57 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
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58 <param name="mt_chromosome" type="hidden" value="MT"/>
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59 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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60 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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61 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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62 </when>
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63 <when value="NCBIM37">
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64 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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65 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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66 <param name="ensembl_genome_version" type="hidden" value="NCBIM37"/>
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67 <param name="ensembl_version" type="hidden" value="67"/>
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68 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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69 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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70 <param name="ucsc_genome_version" type="hidden" value="mm9"/>
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71 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
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72 <param name="mt_chromosome" type="hidden" value="MT"/>
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73 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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74 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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75 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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76 </when>
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77 <when value="Rnor_5.0">
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78 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
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79 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
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80 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
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81 <param name="ensembl_version" type="hidden" value="71"/>
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82 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
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83 <param name="ncbi_prefix" type="hidden" value="Rn"/>
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84 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
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85 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT"/>
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86 <param name="mt_chromosome" type="hidden" value="MT"/>
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87 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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88 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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89 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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90 </when>
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91 <when value="user_specified">
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92 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
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93 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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94 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
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95 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
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96 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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97 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
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98 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
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99 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
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100 <help> Examples:
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101 Homo_sapiens: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
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102 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT
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103 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT
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104 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
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105 </help>
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106 </param>
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107 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
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108 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" />
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109 <param name="ig_gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene" label="IG Gene sources" />
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110 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
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111 </when>
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112 </conditional>
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113 </inputs>
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114 <outputs>
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115 <data format="defuse.conf" name="config_txt" label="${tool.name} on ${genome.ensembl_genome_version} : config.txt"/>
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116 </outputs>
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117 <stdio>
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118 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
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119 <regex match="Error:"
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120 source="both"
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121 level="fatal"
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122 description="Error running Create DeFuse Reference" />
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123
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124 </stdio>
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125 <configfiles>
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126 <configfile name="defuse_config">
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127 #
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128 # Configuration file for defuse
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129 #
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130 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
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131 # will be set by the runtime script using the ENV PATH
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132 #
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133
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134 # Directory where the defuse code was unpacked
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135 source_directory = __DEFUSE_PATH__
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136
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137 # Organism IDs
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138 ensembl_organism = $genome.ensembl_organism
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139 ensembl_prefix = $genome.ensembl_prefix
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140 ensembl_version = $genome.ensembl_version
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141 ensembl_genome_version = $genome.ensembl_genome_version
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142 ucsc_genome_version = $genome.ucsc_genome_version
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143 ncbi_organism = $genome.ncbi_organism
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144 ncbi_prefix = $genome.ncbi_prefix
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145
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146 # Directory where you want your dataset
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147 dataset_directory = $config_txt.extra_files_path
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148
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149 #raw
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150 # Input genome and gene models
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151 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
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152 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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153
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154 # Repeat table from ucsc genome browser
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155 repeats_filename = $(dataset_directory)/repeats.txt
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156
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157 # EST info downloaded from ucsc genome browser
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158 est_fasta = $(dataset_directory)/est.fa
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159 est_alignments = $(dataset_directory)/intronEst.txt
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160
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161 # Unigene clusters downloaded from ncbi
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162 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
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163 #end raw
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164
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165 # Paths to external tools
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166 samtools_bin = __SAMTOOLS_BIN__
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167 bowtie_bin = __BOWTIE_BIN__
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168 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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169 blat_bin = __BLAT_BIN__
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170 fatotwobit_bin = __FATOTWOBIT_BIN__
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171 gmap_bin = __GMAP_BIN__
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172 gmap_setup_bin = __GMAP_SETUP_BIN__
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173 r_bin = __R_BIN__
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174 rscript_bin = __RSCRIPT_BIN__
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175
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176 #raw
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177 # Directory where you want your dataset
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178 gmap_index_directory = $(dataset_directory)/gmap
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179 #end raw
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180
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181 #raw
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182 # Dataset files
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183 dataset_prefix = $(dataset_directory)/defuse
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184 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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185 exons_fasta = $(dataset_prefix).exons.fa
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186 cds_fasta = $(dataset_prefix).cds.fa
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187 cdna_regions = $(dataset_prefix).cdna.regions
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188 cdna_fasta = $(dataset_prefix).cdna.fa
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189 reference_fasta = $(dataset_prefix).reference.fa
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190 rrna_fasta = $(dataset_prefix).rrna.fa
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191 ig_gene_list = $(dataset_prefix).ig.gene.list
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192 repeats_regions = $(dataset_directory)/repeats.regions
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193 est_split_fasta1 = $(dataset_directory)/est.1.fa
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194 est_split_fasta2 = $(dataset_directory)/est.2.fa
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195 est_split_fasta3 = $(dataset_directory)/est.3.fa
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196 est_split_fasta4 = $(dataset_directory)/est.4.fa
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197 est_split_fasta5 = $(dataset_directory)/est.5.fa
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198 est_split_fasta6 = $(dataset_directory)/est.6.fa
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199 est_split_fasta7 = $(dataset_directory)/est.7.fa
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200 est_split_fasta8 = $(dataset_directory)/est.8.fa
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201 est_split_fasta9 = $(dataset_directory)/est.9.fa
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202
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203 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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204 prefilter1 = $(unigene_fasta)
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205
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206 # deFuse scripts and tools
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207 scripts_directory = $(source_directory)/scripts
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208 tools_directory = $(source_directory)/tools
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209 data_directory = $(source_directory)/data
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210 #end raw
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211
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212 # Parameters for building the dataset
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213 chromosomes = $genome.chromosomes
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214 mt_chromosome = $genome.mt_chromosome
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215 gene_sources = $genome.gene_sources
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216 ig_gene_sources = $genome.ig_gene_sources
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217 rrna_gene_sources = $genome.rrna_gene_sources
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218
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219 #raw
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220 # Remove temp files
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221 remove_job_files = yes
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222 remove_job_temp_files = yes
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223 #end raw
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224 </configfile>
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225 <configfile name="defuse_script">
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226 #!/bin/bash
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227 ## define some things for cheetah proccessing
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228 #set $amp = chr(38)
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229 #set $gt = chr(62)
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230 ## substitute pathnames into config file
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231 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
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232 if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
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233 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
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234 if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
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235 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
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236 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
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237 if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
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238 if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
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239 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
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240 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
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241 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
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242 ## copy config to output
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243 cp $defuse_config $config_txt
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244 ## make a data_dir and ln -s the input fastq
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245 mkdir -p $config_txt.extra_files_path
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246 ## create_reference_dataset.pl
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247 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
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248 </configfile>
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249 </configfiles>
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250
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251 <tests>
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252 </tests>
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253 <help>
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254 **DeFuse**
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255
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256 DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. See the DeFuse_Version_0.6_ manual for details.
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257
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258 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.6_:
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259 - genome_fasta from Ensembl
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260 - gene_models from Ensembl
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261 - repeats_filename from UCSC RepeatMasker rmsk.txt
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262 - est_fasta from UCSC
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263 - est_alignments from UCSC intronEst.txt
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264 - unigene_fasta from NCBI
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265
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266 The create_defuse_reference Galaxy tool downloads the reference genome and other source files, and builds any derivative files including bowtie indices, gmap indices, and 2bit files. Expect this step to take at least 12 hours.
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267
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268
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269 It will generate a config.txt file that can be input into the deFuse Galaxy tool.
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270
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271 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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272
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273 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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274
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275 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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277 ------
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278
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279 **Outputs**
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280
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281 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
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282
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283 </help>
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284 </tool>